We haven't made any significant progress on a MS2-to-MS3 guide. I have some rough notes but nothing that's in publishable form. If you have anything you'd like to contribute and have us take a look at, we'd be happy to do so and look at including in the documentation for MiServer 3.

As we've already been communicating via email regarding this, I suggest we continue this discussion using email. Once we've gone through the conversion process, I'll publish guidelines on the steps to take.